Tris-borate buffer (TBE) was advantageous for obtaining a higher resolution of smaller DNA fragments on agarose gels,
when compared to the conventional tris-acetate buffer (TAE). Critical DNA sizes and gel concentrations for a clear
separation were about 2-kb for the 0.8% agarose and 300-bp for the 2.0% agarose. DNA fragments larger than the critical
size (>2-kb on 0.8% agarose gel) migrate faster in TAE, and the smaller fragments (<300-bp on 2% agarose gel)
migrate faster in TBE showing the better resolution in a mini chamber system (Mupid-21).

INTRODUCTION

DNA mobility on agarose gel-electrophoresis is known to depend on the composition and ionic strength of electrode
buffer as well as the agarose concentrations. Tris-acetate buffer (TAE) is a most commonly used running buffer for
preparative work (1, 2). The resolution of supercoiled DNAs is better in TAE than tris-borate buffer (TBE) (3).
However, TAE¡Çs buffering capacity is rather low, and it tends to become exhausted during successive electrophoresis.
In contrast, TBE has a more stable and higher buffering capacity, while eliciting a low recovery of nucleic acid due
to its sticky interaction with agarose (2). Although a popular laboratory manual described that double stranded
linear DNA fragments migrate approximately 10 % faster in TAE than in TBE (4), the small DNA fragments were not
always following the rule. In this study, we employed TAE or TBE as an electrophoresis buffer and DNA size markers
to compare the electrophoretic mobility as a practical bench mark for the benefit of a routine work in a laboratory.

We analyzed two kinds of DNA size markers on the different concentrations of agarose gels containing TAE or
TBE buffers. lambdaDNA/HindIII fragments (23.1 to 0.6-kb) were analyzed on the 0.8 % agarose gels. phiX174
RF DNA /HaeIII fragments (1353 to 72-bp) are analyzed on 2.0 % agarose gels. It was clear that relatively
large DNA fragments (>2-kb on the 0.8 % agarose gel and >300 bp on 2.0 % agarose gel) were well separated on
the gels in TAE buffer than TBE buffer (Fig. 1). Conversely, we encountered the poor separation of smaller (<2-kb
on 0.8 % agarose gel and <300-bp on 2.0 % agarose gel) in TAE buffer. The smaller DNA fragments were more clearly
separated in TBE buffer (Fig. 1. lanes 6-10) than TAE buffer on each gel concentration (Fig. 1. lanes 1-5). Large
DNA fragments (23.1 to 2-kb) migrated faster in TAE than in TBE buffer on 0.8 % agarose gels, and small fragments
(2 to 0.6-kb) migrated faster in TBE than in TAE buffer. The crossing point on the graph dropped on 2-kb in length
(Fig. 2. A). Relatively large DNA fragments (1353 to 300-bp) migrated faster in TAE than in TBE buffer. The crossing
point on the graph showed 300-bp in length (Fig. 2. B).
In conclusion, TBE buffer was effective to obtain high resolution of smaller DNA fragments (300-bp), and TAE buffer
was useful for larger DNA fragments (<2.0-kb) in the mini chamber system (MupidTM-21). The conventional buffer,
TAE, is not always the best choice for gel electrophoresis. Considering the fragment size of DNA, an adequate
electrophoretic condition has to be chosen , i.e., TAE buffer is for larger DNAs than 2-kb in 0.8 % agarose,
and TBE for smaller DNAs than 300-bp in 2.0 % agarose. Either buffer, TBE or TAE, is applicable for the middle
size the DNA fragments ranging from 300-bp to 20-kb. The relative mobility varied according to the size of DNA
fragments, the concentration of agarose, and the composition of electrophoresis buffer. Although the DNA fragments
were generally believed to migrate faster in TAE than in TBE, the smaller fragments were not always the case.
They could migrate faster in TBE than in TAE. ¡ÈThis was sometime a paradox,
but now the time gives it proof¡É(5). Very recently, Stellwagen and colleagues have
given a possible explanation to show the paradox (6, 7). The higher mobility of small fragments in TBE may be
attributed to the formation of nonspecific, highly charged deoxyribose-borate complexes (7).